Professor Les Baillie and his team at the National Botanic Garden of Wales. Photograph: James Davies

Who knows what medicinal secrets lurk in a pot of honey? Scientists in Wales intend finding out and are asking beekeepers throughout the UK to send in their honey for inspection. They're especially keen to know what plants their bees have been feeding on – information that could, in time, help to develop new antibacterial drugs.

Researchers at Cardiff University and the National Botanic Garden of Wales (NBGW) plan to construct a detailed profile of the nation's honey. By analysing each sample, they aim to identify plants that can help to fight antibiotic-resistant bacteria such as MRSA, scourge of many a hospital ward; and also diseases ravaging the bee population.

At the university's Welsh School of Pharmacy, work has just begun on screening samples of honey collected from different locations across the UK. The first stage is to see if the honey can conquer MRSA and Clostridium difficile. There's a straightforward test: honey is mixed with the bacteria and if these are killed off by antimicrobial activity within the honey, this indicates the medicinal potential of the bees' plant food.

The second key piece of work is to identify the plants that show up in the most potent antibacterial honeys. This will be done using a DNA-based identification method developed by the National Botanic Garden.

Long-term, the research aims to point a way towards creating drugs through the plants rather than the honey itself. Les Baillie, professor of microbiology at Cardiff University, sees tackling bugs such as MRSA with new plant-based products as an urgent matter. "We're running out of ways of treating them," he says. "We're living with the legacy of the past – the inappropriate use of antibiotics through buying them on the internet and using them in animal feed."

Honey has been used as a medicine since time immemorial, yet the science of its therapeutic properties is little understood. So far, Baillie's team has acquired more than 50 jars to work on, mainly from supermarkets and Welsh beekeepers, along with a handful from England.

Samples have been passed on to the NBGW. There, plants contained in the most powerful honeys will be identified by a DNA profiling process that has already "barcoded" Wales's 1,143 species of flowering plants.

The usual pattern of drug development entails an expensive laboratory screening of many plant products, often without success. "We're hoping to cut out the middle man and let the bees do a lot of the hard work, guiding to us those plants which work," says Baillie.

Another focus of the research is to try to find honeys with plant constituents that could help bees to resist pests such as the Varroa mite, which has ravaged the UK bee population, and American foulbrood, a destructive infectious disease that attacks bee larvae throughout the world.

"Honey at its most basic is concentrated sugar, but even that can do nasty things to bugs, sucking the water out of them," says Baillie. Antibacterial activity is linked to factors such as the presence of phytochemicals, which derive from plants visited by bees. These include chemicals that are produced by plants as protection against pathogens (organisms that cause disease). "We hope to identify compounds that will also target pathogens of humans and bees," says Baillie.

In the past, honey has been used as a medicine on a "try it and see" basis. Baillie believes most of the science is unknown: "we've only scratched the surface of the biology". The research is currently being financed by the Society for Applied Microbiology and will, from October, be supported by the European Social Fund and the Welsh government.

Baillie is now on the hunt for a PhD student to work on the project full-time. Meanwhile, his early screening of samples has already yielded honeys with antimicrobial properties that can kill MRSA.

Who knows what chance the Welsh research project has of isolating a plant with similar properties to manuka, celebrated for its antibacterial potency and used in medication to treat wounds? "If you don't look, you don't find," says Dr Natasha de Vere, head of conservation and research at NBGW. "While some plants are closely related, their chemical properties are quite different, so there's all to play for."

Around half of Wales's flowering plant varieties are insect-pollinated and de Vere is keen to get samples of honey from the same hive at different times of the year. DNA extraction is likely to begin in the next couple of weeks after samples have been through the bar-coding process.

NBGW has a detailed biological record of every Welsh flowering plant on its database. This has been built up by using sections of DNA that enable any species to be identified from the tiniest fragment of leaf, seed or pollen grain; and also at different life stages, or from a mixture of samples.

Aside from the latest research, Wales has long focused on studying the value of honey for use in dressing wounds. Professor Rose Cooper, of the University of Wales Institute, Cardiff's microbiology and infection group, has focused on manuka honey, but also examined other honeys from Britain and abroad.

Although people have been tempted into home experiments with cheap honey, Cooper's team found that more than half – 10 out of 18 – samples examined failed to display any antibacterial activity because they lacked the necessary constituent plants. And while the quality of honey used in the manufacture of licensed wound-care products is regulated, supermarket honey is not regulated for medical use. The possibility of infecting vulnerable patients exists, Cooper warns.

Soon the fog over what works – and why – may be lifted , though understanding the potential of what's under your nose can take time. "It wasn't until the 1950s that the medical properties of daffodils were fully appreciated," says de Vere. "Research has since developed a chemical, galantamine, that's important in treating Alzheimer's.

"There's an awful lot we don't know. This is one aim of the project – looking at the medicinal properties of the plants to see if there's anything like manuka. We might even be able to make a superhoney."